My question is still though if it would be bad to not raise an exception
when different filetypes are split in the same job.

In general splitting multiple files of different types seems dangerous.
That is presumably the point of the Galaxy exception.
In my example of splitting a pair of FASTQ files, they are the same
format, so Galaxy can make assumptions about how they will be
split. Note splitting into chunks based on the size on disk would
be wrong (e.g. if the forward reads in the first file are all longer
than the reverse reads in the second file).
In the case of splitting a paired FASTA + QUAL file, these are now
different file formats, so more caution is required. In fact both
can be split are the sequence/read level so can be processed.
I think the key requirement here for 'matched' splitting is each
file must have the same number of 'records' (in my example,
sequencing reads, in your case sub-files), and can be split into
a chunks of the same number of 'records'.
Perhaps different file type combinations could be special cases
in the splitter code? Then if there is no dedicated splitter for a
given combination, then that combination cannot be split.
Peter

I could imagine the multi splitter calling some sort of validating
method of the different datatypes to gather information about the
different datasets, e.g. split size, split numbers, matching file types,
before executing a split. There may be more and better ways to get
around it though. I'll settle for disabling the check now, if mainline
galaxy would be interested we could look at it further I guess.